相关论文: A methodology of quantifying membrane permeability…
The relative energies of different phases or polymorphs of molecular solids can be small, less than a kiloJoule/mol. Reliable description of such energy differences requires high quality treatment of electron correlations, typically beyond…
Renewal theory is finding increasing applications in non-equilibrium statistical physics. One example relates the probability density and survival probability of a Brownian particle or an active run-and-tumble particle with stochastic…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
We propose a model describing liquid-solid phase coexistence in mixed lipid membranes by including explicitly the occurrence of a rippled phase. For a single component membrane, we employ a previous model in which the membrane thickness is…
We consider a discrete-continuum model of a biomembrane with embedded particles. While the membrane is represented by a continuous surface, embedded particles are described by rigid discrete objects which are free to move and rotate in…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Values of water permeability for cementitious materials reported in the literature show a large scatter. This is partially attributed to the fact that materials used in different studies are different. To eliminate the effects of cements,…
Polymer blends consisting of two or more polymers are important for a wide variety of industries and processes, but, the precise mechanism of their thermomechanical behaviour is incompletely understood. In order to understand clearly, it is…
A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads…
Understanding the migration and trapping of CO$_2$ in the subsurface is vital to geologic carbon storage projects. Traditional characterization methods employ steady-state co-injection experiments to determine relative permeability and…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Membranes regulate transport in a wide variety of industrial and biological applications. The microscale geometry of the membrane can significantly affect overall transport through the membrane, but the precise nature of this multiscale…
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the…
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly construction of a bias potential that is function of a selected number of collective variables. We propose here a change in perspective that shifts the…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the $\lambda$--$\newrho$ model for irreversible…
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of…
The interface between liquid water and the Pt(111) metal surface is characterized structurally and thermodynamically via reactive molecular dynamics (MD) simulations within the ReaxFF framework. The formation of a distinct buckled adsorbate…
The diffusion coefficient of a circular shaped inclusion in a liquid membrane is investigated by taking into account the interaction between membranes and bulk solvents of arbitrary thickness. As illustrative examples, the diffusion…
The pH value in bioethanol is a quality control parameter related to its acidity and to the corrosiveness of vehicle engines when it is used as fuel. In order to verify the comparability and reliability of the measurement of pH in…